Scientific Knowledge Object Patterns

Web technology is revolutionizing the way diverse scientific knowledge is produced and disseminated. In the past few years, a handful of discourse representation models have been proposed for the externalization of the rhetoric and argumentation captured within scientific publications. However, there hasn’t been a unified interoperable pattern that is commonly used in practice by publishers and individual users yet. In this paper, we introduce the Scientific Knowledge Object Patterns (SKO Patterns) towards a general scientific discourse representation model, especially for managing knowledge in emerging social web and semantic web. © ACM, 2011. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version is going to be published in "Proceedings of 15th European Conference on Pattern Languages of Programs", (2011) http://portal.acm.org/event.cfm?id=RE197&CFID=8795862&CFTOKEN=1476113

Automated ontology population and enrichment of scientific publications

Scientific publications are the most important resources available to the research communities. Researchers want their work to be widely recognized and available and also need powerful search engines to identify other publications and researchers working in the same area. Therefore, a good representation and organization of scientific products is crucial for an accurate retrieval of information. This paper describes an approach for automated population and semantic enrichment of an ontology model that represents scientific publications. Specifically, the type of enrichment used in this approach consists of implementing semantic similarity measurements between publications. Several experiments were performed to identify the best similarity measurement, using a statistical approach and the precision of the measurements

RegenBase: a knowledge base of spinal cord injury biology for translational research.

Spinal cord injury (SCI) research is a data-rich field that aims to identify the biological mechanisms resulting in loss of function and mobility after SCI, as well as develop therapies that promote recovery after injury. SCI experimental methods, data and domain knowledge are locked in the largely unstructured text of scientific publications, making large scale integration with existing bioinformatics resources and subsequent analysis infeasible. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. To address these challenges, we have developed RegenBase, a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase uses consistent identifier schemes and data representations that enable automated linking among RegenBase statements and also to other biological databases and electronic resources. By querying RegenBase, we have identified novel biological hypotheses linking the effects of perturbagens to observed behavioral outcomes after SCI. RegenBase is publicly available for browsing, querying and download.Database URL:http://regenbase.org

A short survey of discourse representation models

With the advancement of technology and the wide adoption of ontologies as knowledge representation formats, in the last decade, a handful of models were proposed for the externalization of the rhetoric and argumentation captured within scientific publications. Conceptually, most of these models share a similar representation form of the scientific publication, i.e. as a series of interconnected elementary knowledge items. The main differences are given by the terminology used, the types of rhetorical and/or argumentation relations connecting the knowledge items and the foundational theories supporting these relations. This paper analyzes the state of the art and provides a concise comparative overview of the five most prominent discourse representation models, with the goal of sketching an unified model for discourse representation

Mining Scholarly Data for Fine-Grained Knowledge Graph Construction

Knowledge graphs (KG) are large network of entities and relationships, tipically expressed as RDF triples, relevant to a specific domain or an organization. Scientific Knowledge Graphs (SKGs) focus on the scholarly domain and typically contain metadata describing research publications such as authors, venues, organizations, research topics, and citations. The next big challenge in this field regards the generation of SKGs that also contain a explicit representation of the knowledge presented in research publications. In this paper, we present a preliminary approach that uses a set of NLP and Deep Learning methods for extracting entities and relationships from research publications and then integrates them in a KG. More specifically, we i) tackle the challenge of knowledge extraction by employing several state-of-the-art Natural Language Processing and Text Mining tools, ii) describe an approach for integrating entities and relationships generated by these tools, iii) analyse an automatically generated Knowledge Graph including 10, 425 entities and 25, 655 relationships derived from 12, 007 publications in the field of Semantic Web, and iv) discuss how Deep Learning methods can be applied to overcome some limitations of the current techniques

Ontology-Based Recommendation of Editorial Products

Major academic publishers need to be able to analyse their vast catalogue of products and select the best items to be marketed in scientific venues. This is a complex exercise that requires characterising with a high precision the topics of thousands of books and matching them with the interests of the relevant communities. In Springer Nature, this task has been traditionally handled manually by publishing editors. However, the rapid growth in the number of scientific publications and the dynamic nature of the Computer Science landscape has made this solution increasingly inefficient. We have addressed this issue by creating Smart Book Recommender (SBR), an ontology-based recommender system developed by The Open University (OU) in collaboration with Springer Nature, which supports their Computer Science editorial team in selecting the products to market at specific venues. SBR recommends books, journals, and conference proceedings relevant to a conference by taking advantage of a semantically enhanced representation of about 27K editorial products. This is based on the Computer Science Ontology, a very large-scale, automatically generated taxonomy of research areas. SBR also allows users to investigate why a certain publication was suggested by the system. It does so by means of an interactive graph view that displays the topic taxonomy of the recommended editorial product and compares it with the topic-centric characterization of the input conference. An evaluation carried out with seven Springer Nature editors and seven OU researchers has confirmed the effectiveness of the solution

Hypotheses, evidence and relationships: The HypER approach for representing scientific knowledge claims

Biological knowledge is increasingly represented as a collection of (entity-relationship-entity) triplets. These are queried, mined, appended to papers, and published. However, this representation ignores the argumentation contained within a paper and the relationships between hypotheses, claims and evidence put forth in the article. In this paper, we propose an alternate view of the research article as a network of 'hypotheses and evidence'. Our knowledge representation focuses on scientific discourse as a rhetorical activity, which leads to a different direction in the development of tools and processes for modeling this discourse. We propose to extract knowledge from the article to allow the construction of a system where a specific scientific claim is connected, through trails of meaningful relationships, to experimental evidence. We discuss some current efforts and future plans in this area